The Amarnath Yatra was temporarily suspended after a cloudburst hit near the base camp of the holy cave shrine in south Kashmir Himalayas on Friday.
The cloudburst hit the cave area at around 5.30 pm after heavy rains, officials said.
Police and other civil administration have launched a rescue operation as some langars were affected by the gushing waters, they added.
According to reports, at least five people have died and many are missing.
Union Home Minister Amit Shah said he has spoken to Jammu and Kashmir Lieutenant Governor Manoj Sinha and inquired about the situation.
"NDRF, CRPF, BSF and local administration are engaged in the rescue work. Saving people's lives is our priority," he said.